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- PDB-8gai: Cavia porcellus (guinea pig) importin-alpha 1 in complex with Bim... -

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Basic information

Entry
Database: PDB / ID: 8gai
TitleCavia porcellus (guinea pig) importin-alpha 1 in complex with Bimax2 peptide
Components
  • Bimax2
  • Importin subunit alpha
KeywordsTRANSPORT PROTEIN / Complex / inhibitor
Function / homology
Function and homology information


entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / NLS-bearing protein import into nucleus / nuclear localization sequence binding / nuclear import signal receptor activity / positive regulation of type I interferon production / histone deacetylase binding / host cell / nuclear membrane ...entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / NLS-bearing protein import into nucleus / nuclear localization sequence binding / nuclear import signal receptor activity / positive regulation of type I interferon production / histone deacetylase binding / host cell / nuclear membrane / nucleoplasm / cytosol
Similarity search - Function
Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats ...Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha
Similarity search - Component
Biological speciesCavia porcellus (domestic guinea pig)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsHawker, J.E. / Forwood, J.K. / Donnelly, C.M. / Stewart, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Cavia porcellus (guinea pig) importin-alpha 1 in complex with bimax2 peptide
Authors: Hawker, J.E. / Donnelly, C.M. / Stewart, M. / Forwood, J.K.
History
DepositionFeb 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Importin subunit alpha
B: Bimax2
C: Importin subunit alpha
D: Bimax2


Theoretical massNumber of molelcules
Total (without water)110,3514
Polymers110,3514
Non-polymers00
Water1,13563
1
A: Importin subunit alpha
B: Bimax2


Theoretical massNumber of molelcules
Total (without water)55,1752
Polymers55,1752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Importin subunit alpha
D: Bimax2


Theoretical massNumber of molelcules
Total (without water)55,1752
Polymers55,1752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.008, 99.269, 123.759
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Importin subunit alpha


Mass: 51239.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cavia porcellus (domestic guinea pig) / Gene: KPNA2 / Production host: Escherichia coli (E. coli) / References: UniProt: H0VVB1
#2: Protein/peptide Bimax2


Mass: 3936.440 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG6000, 0.1M sodium acetate, 0.2M ammonium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.65→19.95 Å / Num. obs: 25741 / % possible obs: 94.5 % / Redundancy: 4.5 % / Biso Wilson estimate: 34.7 Å2 / CC1/2: 0.991 / Χ2: 0.97 / Net I/σ(I): 6.5
Reflection shellResolution: 2.65→2.78 Å / Num. unique obs: 24373 / CC1/2: 0.689

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→19.95 Å / SU ML: 0.3245 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.8488
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2411 1334 5.19 %
Rwork0.2023 24366 -
obs0.2044 25700 93.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.3 Å2
Refinement stepCycle: LAST / Resolution: 2.65→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7056 0 0 63 7119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317227
X-RAY DIFFRACTIONf_angle_d0.66839840
X-RAY DIFFRACTIONf_chiral_restr0.0381170
X-RAY DIFFRACTIONf_plane_restr0.00461270
X-RAY DIFFRACTIONf_dihedral_angle_d12.27632696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.740.28411380.26652435X-RAY DIFFRACTION95.4
2.74-2.850.30381350.24932397X-RAY DIFFRACTION94.2
2.85-2.980.29121300.24582458X-RAY DIFFRACTION95.75
2.98-3.140.29921280.2382480X-RAY DIFFRACTION95.92
3.14-3.340.29361450.23232437X-RAY DIFFRACTION95.24
3.34-3.590.24211290.2232455X-RAY DIFFRACTION94.38
3.59-3.950.24181440.18792395X-RAY DIFFRACTION92.9
3.95-4.520.19831330.15982404X-RAY DIFFRACTION91.82
4.52-5.670.21141240.1772453X-RAY DIFFRACTION92.63
5.67-19.950.20441280.1852452X-RAY DIFFRACTION88.84
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.732098781950.9954272245530.7744985004923.961855596460.3551405251863.00577143284-0.09535742806270.0523855240135-0.4420095843860.002929866505460.0264141063958-0.1485066888950.431723608045-0.03337596995620.02820521847820.2967444061910.05534195022780.02406470853360.274520415339-0.02841417056360.288552504639-24.96310952-6.2581523649-19.0818949862
20.283946048222-0.450735480974-0.7341867422562.317269099092.417074843463.85433894131-0.02127981987730.0720965004126-0.0112810959975-0.198638891264-0.00361321735657-0.0510389772221-0.1835056659420.1108493856250.02119383990050.2488470906290.000240591194138-0.01439162471990.3283951677890.01974545226340.323609388011-24.195968853426.18431803240.450043213955
33.60779277237-0.0906407279597-0.9960064868694.61903913891.307274777635.81455902614-0.0560722869306-0.3672283805660.01654074742340.1958657189660.0433430038597-0.268071554120.2248554319060.6809040765540.02216236259740.2900619368080.0378390997797-0.02432028873730.5273252443990.04244772883720.347760770873-25.839963613736.012286716132.6184994953
44.871443044370.609837663916-4.752490492042.680897827980.586481359795.18450334565-0.37322560923-1.680162587870.2768826913382.036599101790.659075211848-0.9250399604990.595925324961.92177721466-0.2443720464690.7563434337230.183612645671-0.1723329155180.592959211225-0.1348398168670.474922376974-16.874578134225.26902455812.2744794725
52.014051901093.380559082192.238714749249.074995899846.096828647214.11098144421-0.250638652146-2.1385146740.7426676625321.61751101509-1.023493489330.516940878071-0.387575030495-0.8991144110010.8421657110630.858901466199-0.0337553696133-0.03319755577560.970614979684-0.2242099089770.876034470669-26.88153844613.30939955612.18761334382
67.901208694153.316627999244.839164717568.080402571434.568154556593.988040529680.0573692435763-0.6191543617930.2464010272570.173216395052-0.3562681124691.05602752948-0.0604504170431-0.6616043837950.7315628549870.2937834806360.07628878032780.09572125770640.3202519136860.03804358933730.425727154193-32.98730924150.722881289989-13.9206689642
73.76510534657-1.65582775485-0.578740938864.130749233251.550477846673.62630069142-0.085651317870.1109773396870.262263394331-0.2996260462790.00542772975771-0.154887393952-0.360640404947-0.1891888393660.05182586494790.327853216741-0.038445986388-0.01013643375070.349494966751-0.01800031841530.358469604313-29.7833771827-5.5080632134219.8293665764
8-0.07426295188180.0774946314520.03942254129052.737670549012.709729381913.45123110404-0.01671787617090.007678829711330.06228005553030.1243087461080.0548102707005-0.06392223785960.1870688943420.0447996811869-0.06228213574870.338640968919-0.02504527948030.01751477412830.3200431997220.01361942350260.308028018676-29.1281786714-36.15594112344.43108862411
91.52715710648-0.5746328325580.3805470110391.30601587210.8551194802896.12164911060.03286441320770.1221800996530.1341726788690.0372590636990.0634049834321-0.136218316459-0.1105032234040.0538438481186-0.02244906196170.27025971702-0.01957246937470.01255112432570.331399363677-0.009524868435760.319532143896-33.0984559894-46.1608747658-24.0775997596
102.91538713248-2.460616984820.3601808799683.120212441151.292477987982.705987203940.313432420639-0.0985383610662-0.482884104253-0.858547553094-0.3129549918410.0953291184935-1.56530307770.2591606684830.2174894333550.55129664334-0.1352319014480.03833474982470.517111682461-0.06527119811120.564463990597-25.666379386-46.3441363776-41.2717082244
117.953486974226.211323301823.50165873074.847396922052.716172991551.550387043950.7793063546850.832768219493-0.9214394973960.04431898844970.865886294526-0.901647229583-0.2099934829270.425751985762-1.470704553710.655394292568-0.0367707067524-0.0127578900370.737256164616-0.05268055136480.47820072076-17.9544590888-44.8757488321-20.0332289601
122.5400914686-0.491660863772-0.6564358529298.833148599794.475161713542.385816230480.3351249937280.3629123828020.773155524879-1.42256255961-0.5759220256230.781404016135-0.394865190086-0.7919289443890.2819123066990.6386948249320.04763476199030.0384251068950.5008027798560.009175487789660.410462279336-25.6861471635-31.430604533-7.93125945265
136.28142838048-6.59905268636-5.33795035859.471717967186.146960516634.64597856951-0.0769743684110.55308904282-0.379719132796-0.610343795211-0.9208770838670.754135371912-0.5441355384910.06496517734950.6772046300020.4353090418060.06470115590190.01120596058720.542874565208-0.03062638666530.249860208853-37.5537988732-16.14845177710.5101655634
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 76 through 219 )AA76 - 2191 - 144
22chain 'A' and (resid 220 through 433 )AA220 - 433145 - 358
33chain 'A' and (resid 434 through 503 )AA434 - 503359 - 428
44chain 'B' and (resid 8 through 12 )BB8 - 121 - 5
55chain 'B' and (resid 13 through 22 )BB13 - 226 - 15
66chain 'B' and (resid 23 through 29 )BB23 - 2916 - 22
77chain 'C' and (resid 76 through 219 )CC76 - 2191 - 144
88chain 'C' and (resid 220 through 390 )CC220 - 390145 - 315
99chain 'C' and (resid 391 through 481 )CC391 - 481316 - 406
1010chain 'C' and (resid 482 through 509 )CC482 - 509407 - 434
1111chain 'D' and (resid 3 through 7 )DD3 - 71 - 5
1212chain 'D' and (resid 8 through 17 )DD8 - 176 - 15
1313chain 'D' and (resid 18 through 29 )DD18 - 2916 - 27

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